added option --print-protein and --print-protein-pretty

docs/source/annotation_from_genomic_level.rst

@@ -359,43 +359,6 @@ A block-substitution that is in-frame,
       CSQN=Missense;codon_cDNA=508-509-510;source=CCDS
 
 
-Inspect variant protein sequence
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The `--print-protein` and `--print-protein-pretty` options displays the full variant protein sequence in the `variant_protein_seq` field of the info when the genomic variant hits a protein-coding transcript.
-
-.. code:: bash
-
-   $ transvar ganno -i 'chr1:g.115256530G>A' --ensembl --print-protein
-
-::
-
-
-`--print-protein-pretty` output is more human-readable and highlight the mutation in brackets.
-
-.. code:: bash
-
-   $ transvar ganno --ccds -i 'chr3:g.178936091G>A' --print-protein-pretty
-
-::
-
-The alphabet transformation option `--aa3` applies here as well.
-
-.. code:: bash
-
-   $ transvar ganno -i 'chr1:g.115256530G>A' --ensembl --print-protein-pretty --aa3
-
-::
-
-To inspect the protein sequence after a deletion,
-
-.. code:: bash
-
-   $ transvar canno --ccds -i 'CCDS8856:c.769_771delGGG' --print-protein-pretty
-
-::
-
-   
 Promoter region
 ##################
 
@@ -497,8 +460,8 @@ output a splice variation
 
 ::
 
-   chr7:5568790A>G CCDS5341 (protein_coding)       ACTB    -
-      chr7:g.5568790A>G/c.363+2T>C/.       inside_[intron_between_exon_2_and_3]
+   chr7:5568790A>G	CCDS5341 (protein_coding)	ACTB	-
+      chr7:g.5568790A>G/c.363+2T>C/.	inside_[intron_between_exon_2_and_3]
       CSQN=SpliceDonorSNV;C2=SpliceDonorOfExon2_At_chr7:5568791;source=CCDS
 
 

docs/source/index.rst

@@ -18,6 +18,7 @@ Contents:
    annotation_from_protein_level
    annotation_from_cdna_level
    interpret_variant_consequence
+   inspect_variants
    faq
    features
    license

docs/source/inspect_variants.rst

@@ -0,0 +1,165 @@
+***************************
+Inspect variant sequences
+***************************
+
+The `--print-protein` and `--print-protein-pretty` options displays the full variant protein sequence in the `variant_protein_seq` field of the info when the genomic variant hits a protein-coding transcript.
+
+Missense substitution
+#######################
+
+.. code:: bash
+
+   $ transvar ganno -i 'chr1:g.115256530G>A' --ensembl --print-protein
+
+::
+
+   chr1:g.115256530G>A	ENST00000369535 (protein_coding)	NRAS	-
+      chr1:g.115256530G>A/c.181C>T/p.Q61*	inside_[cds_in_exon_3]
+      CSQN=Nonsense;variant_protein_seq=MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQ
+      VVIDGETCLLDILDTAG*;codon_pos=115256528-115256529-115256530;ref_codon_seq=CAA;
+      aliases=ENSP00000358548;source=Ensembl
+
+`--print-protein-pretty` output is more human-readable and highlight the mutation in brackets.
+
+.. code:: bash
+
+   $ transvar ganno --ccds -i 'chr3:g.178936091G>A' --print-protein-pretty
+
+::
+
+   chr3:g.178936091G>A	CCDS43171 (protein_coding)	PIK3CA	+
+      chr3:g.178936091G>A/c.1633G>A/p.E545K	inside_[cds_in_exon_9]
+      CSQN=Missense;dbsnp=rs104886003(chr3:178936091G>A);variant_protein_seq=MPPRPS
+      SGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFF
+      DETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPH
+      SRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSE
+      QLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTA
+      TPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDI
+      YIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNK
+      ETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEIT_
+      _[E>K]__QEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGF
+      AVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESY
+      CRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEE
+      CRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCV
+      GLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIM
+      VKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFI
+      NLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIFHTIKQHALN*;codon_
+      pos=178936091-178936092-178936093;ref_codon_seq=GAG;source=CCDS
+
+
+The alphabet transformation option `--aa3` applies here as well.
+
+.. code:: bash
+
+   $ transvar ganno -i 'chr1:g.115256530G>A' --ensembl --print-protein-pretty --aa3
+
+::
+
+   chr1:g.115256530G>A	ENST00000369535 (protein_coding)	NRAS	-
+      chr1:g.115256530G>A/c.181C>T/p.Gln61X	inside_[cds_in_exon_3]
+      CSQN=Missense;variant_protein_seq=MetThrGluTyrLysLeuValValValGlyAlaGlyGlyValG
+      lyLysSerAlaLeuThrIleGlnLeuIleGlnAsnHisPheValAspGluTyrAspProThrIleGluAspSerTyr
+      ArgLysGlnValValIleAspGlyGluThrCysLeuLeuAspIleLeuAspThrAlaGly__[GluGluTyrSerAl
+      aMetArgAspGlnTyrMetArgThrGlyGluGlyPheLeuCysValPheAlaIleAsnAsnSerLysSerPheAlaA
+      spIleAsnLeuTyrArgGluGlnIleLysArgValLysAspSerAspAspValProMetValLeuValGlyAsnLys
+      CysAspLeuProThrArgThrValAspThrLysGlnAlaHisGluLeuAlaLysSerTyrGlyIleProPheIleGl
+      uThrSerAlaLysThrArgGlnGlyValGluAspAlaPheTyrThrLeuValArgGluIleArgGlnTyrArgMetL
+      ysLysLeuAsnSerSerAspAspGlyThrGlnGlyCysMetGlyLeuProCysValValMet>X];codon_pos=1
+      15256528-115256529-115256530;ref_codon_seq=CAA;aliases=ENSP00000358548;source
+      =Ensembl
+
+Deletion
+############
+
+.. code:: bash
+
+   $ transvar canno --ccds -i 'CCDS8856:c.769_771delGGG' --print-protein-pretty
+
+::
+
+   CCDS8856:c.769_771delGGG	CCDS8856 (protein_coding)	AAAS	-
+      chr12:g.53703427_53703429delCCC/c.769_771delGGG/p.G257delG	inside_[cds_in_exon_8]
+      CSQN=InFrameDeletion;left_align_gDNA=g.53703424_53703426delCCC;unaligned_gDNA
+      =g.53703424_53703426delCCC;left_align_cDNA=c.766_768delGGG;unalign_cDNA=c.769
+      _771delGGG;left_align_protein=p.G256delG;unalign_protein=p.G257delG;variant_p
+      rotein_seq=MCSLGLFPPPPPRGQVTLYEHNNELVTGSSYESPPPDFRGQWINLPVLQLTKDPLKTPGRLDHGTR
+      TAFIHHREQVWKRCINIWRDVGLFGVLNEIANSEEEVFEWVKTASGWALALCRWASSLHGSLFPHLSLRSEDLIAEF
+      AQVTNWSSCCLRVFAWHPHTNKFAVALLDDSVRVYNASSTIVPSLKHRLQRNVASLAWKPLSASVLAVACQSCILIW
+      TLDPTSLSTRPSSGCAQVLSHPGHTPVTSLAWAPSG__[G_deletion]__RLLSASPVDAAIRVWDVSTETCVPL
+      PWFRGGGVTNLLWSPDGSKILATTPSAVFRVWEAQMWTCERWPTLSGRCQTGCWSPDGSRLLFTVLGEPLIYSLSFP
+      ERCGEGKGCVGGAKSATIVADLSETTIQTPDGEERLGGEAHSMVWDPSGERLAVLMKGKPRVQDGKPVILLFRTRNS
+      PVFELLPCGIIQGEPGAQPQLITFHPSFNKGALLSVGWSTGRIAHIPLYFVNAQFPRFSPVLGRAQEPPAGGGGSIH
+      DLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL*;source=CCDS
+
+Insertion
+############
+
+.. code:: bash
+
+   $ transvar ganno -i 'chr2:g.69741762_69741763insTGC' --ccds --print-protein-pretty
+
+::
+
+   chr2:g.69741762_69741763insTGC	CCDS1893 (protein_coding)	AAK1	-
+      chr2:g.69741780_69741782dupCTG/c.1614_1616dupGCA/p.Q546dupQ	inside_[cds_in_exon_12]
+      CSQN=InFrameInsertion;left_align_gDNA=g.69741762_69741763insTGC;unalign_gDNA=
+      g.69741762_69741763insTGC;left_align_cDNA=c.1596_1597insCAG;unalign_cDNA=c.16
+      14_1616dupGCA;left_align_protein=p.Y532_Q533insQ;unalign_protein=p.Q539dupQ;v
+      ariant_protein_seq=MKKFFDSRREQGGSGLGSGSSGGGGSTSGLGSGYIGRVFGIGRQQVTVDEVLAEGGFA
+      IVFLVRTSNGMKCALKRMFVNNEHDLQVCKREIQIMRDLSGHKNIVGYIDSSINNVSSGDVWEVLILMDFCRGGQVV
+      NLMNQRLQTGFTENEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLHDRGHYVLCDFGSATNKFQNPQTEGVNA
+      VEDEIKKYTTLSYRAPEMVNLYSGKIITTKADIWALGCLLYKLCYFTLPFGESQVAICDGNFTIPDNSRYSQDMHCL
+      IRYMLEPDPDKRPDIYQVSYFSFKLLKKECPIPNVQNSPIPAKLPEPVKASEAAAKKTQPKARLTDPIPTTETSIAP
+      RQRPKAGQTQPNPGILPIQPALTPRKRATVQPPPQAAGSSNQPGLLASVPQPKPQAPPSQPLPQTQAKQPQAPPTPQ
+      QTPSTQAQGLPAQAQATPQHQQQLFLKQQQQQQQPPPAQQQPAGTFYQQQQAQTQQFQAVHPATQKPAIAQFPVVSQ
+      GGSQQQLMQNFYQQQQQQQQQQQQQQ__[insert_Q]__LATALHQQQLMTQQAALQQKPTMAAGQQPQPQPAAAP
+      QPAPAQEPAIQAPVRQQPKVQTTPPPAVQGQKVGSLTPPSSPKTQRAGHRRILSDVTHSAVFGVPASKSTQLLQAAA
+      AEASLNKSKSATTTPSGSPRTSQQNVYNPSEGSTWNPFDDDNFSKLTAEELLNKDFAKLGEGKHPEKLGGSAESLIP
+      GFQSTQGDAFATTSFSAGTAEKRKGGQTVDSGLPLLSVSDPFIPLQVPDAPEKLIEGLKSPDTSLLLPDLLPMTDPF
+      GSTSDAVIEKADVAVESLIPGLEPPVPQRLPSQTESVTSNRTDSLTGEDSLLDCSLLSNPTTDLLEEFAPTAISAPV
+      HKAAEDSNLISGFDVPEGSDKVAEDEFDPIPVLITKNPQGGHSRNSSGSSESSLPNLARSLLLVDQLIDL*;phase
+      =2;source=CCDS
+
+
+Frameshift sequence
+######################
+
+.. code:: bash
+
+   $ transvar canno --ccds -i 'CCDS8856:c.769_770delGG' --print-protein-pretty
+
+::
+
+   CCDS8856:c.769_770delGG	CCDS8856 (protein_coding)	AAAS	-
+      chr12:g.53703428_53703429delCC/c.770_771delGG/p.G257Afs*65	inside_[cds_in_exon_8]
+      CSQN=Frameshift;left_align_gDNA=g.53703424_53703425delCC;unaligned_gDNA=g.537
+      03425_53703426delCC;left_align_cDNA=c.766_767delGG;unalign_cDNA=c.769_770delG
+      G;variant_protein_seq=MCSLGLFPPPPPRGQVTLYEHNNELVTGSSYESPPPDFRGQWINLPVLQLTKDPL
+      KTPGRLDHGTRTAFIHHREQVWKRCINIWRDVGLFGVLNEIANSEEEVFEWVKTASGWALALCRWASSLHGSLFPHL
+      SLRSEDLIAEFAQVTNWSSCCLRVFAWHPHTNKFAVALLDDSVRVYNASSTIVPSLKHRLQRNVASLAWKPLSASVL
+      AVACQSCILIWTLDPTSLSTRPSSGCAQVLSHPGHTPVTSLAWAPSG__[frameshift_GRLLSASPVDAAIRVW
+      DVSTETCVPLPWFRGGGVTNLLWSPDGSKILATTPSAVFRVWEAQMWTCERWPTLSGRCQTGCWSPDGSRLLFTVLG
+      EPLIYSLSFPERCGEGKGCVGGAKSATIVADLSETTIQTPDGEERLGGEAHSMVWDPSGERLAVLMKGKPRVQDGKP
+      VILLFRTRNSPVFELLPCGIIQGEPGAQPQLITFHPSFNKGALLSVGWSTGRIAHIPLYFVNAQFPRFSPVLGRAQE
+      PPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL*>AAALSFTRGCCYPGMGCLNRDLCPPSLVPRRW
+      GDQPALVPRRQQNPGYHSFSCLSSLGGPDVDL*];source=CCDS
+
+
+.. code:: bash
+
+   $ transvar canno -i 'CCDS54438:c.409_421del' --ccds --print-protein-pretty
+
+::
+
+   CCDS54438:c.409_421del	CCDS54438 (protein_coding)	ATG16L1	+
+      chr2:g.234183368_234183380del13/c.409_421del13/p.T137Lfs*5	inside_[cds_in_exon_5]
+      CSQN=Frameshift;left_align_gDNA=g.234183367_234183379del13;unaligned_gDNA=g.2
+      34183368_234183380del13;left_align_cDNA=c.408_420del13;unalign_cDNA=c.409_421
+      del13;variant_protein_seq=MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSV
+      LAQKLQAEKHDVPNRHEIRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATRRSVSSF
+      PVPQDNVD__[frameshift_THPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGE
+      KCEFKGSLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRT
+      LKLWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSR
+      DDLLKVIDLRTNAIKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLYIWSVLTGKVEKVLSKQHSSSINAVAW
+      SPSGSHVVSVDKGCKAVLWAQY*>LVKK*];source=CCDS
+

setup.py

@@ -1,6 +1,9 @@
 #!/usr/bin/env python
 
 # The MIT License
+#
+# Copyright (c) 2016
+# Wanding Zhou
 # 
 # Copyright (c) 2014, 2015 The University of Texas MD Anderson Cancer Center
 # Wanding Zhou, Tenghui Chen and Ken Chen
@@ -25,7 +28,7 @@
 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 #
-# Contact: Ken Chen <[email protected]>
+# Contact: Wanding Zhou <[email protected]>
 
 import os
 import sys

test/test.sh

@@ -25,6 +25,13 @@ colordiff testout/ganno_tamborero.vcf
 
 transvar ganno -l data/tamborero_data/transvar_dna_input.txt --ensembl | tee testout/ganno_tamborero_output
 
+## upload github
+
+modify transvar/version.py
+git commit -am "this version"
+git tag -a v[version] -m "version [version]"
+git push --tag
+
 ## register testpypi
 
 python setup.py register -r https://testpypi.python.org/pypi

transvar/deletion.py

@@ -24,14 +24,14 @@
 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-
 """
 
 from transcripts import *
 from utils import *
 from record import *
 from copy import copy
 from describe import *
+from proteinseqs import *
 
 # TODO: refactor left-right align
 class GNucDeletion():
@@ -315,28 +315,16 @@ def taa_del_id(t, taa_beg, taa_end, args):
 
     return s
 
-def variant_protein_sequence_deletion(r, t, args, taa_beg, taa_end):
-
-    if args.pp or args.ppp:
-        pp = list(aaf(t.get_proteinseq(), args, use_list=True))
-        if args.pp:
-            del pp[taa_beg-1:taa_end]
-        elif args.ppp:
-            delseq = ''.join(pp[taa_beg-1:taa_end])
-            del pp[taa_beg-1:taa_end]
-            pp.insert(taa_beg-1, '__[%s_deletion]__' % delseq)
-        r.append_info('variant_protein_seq=%s' % ''.join(pp))
-
 def taa_set_del(r, t, taa_beg, taa_end, args):
 
     i1r, i2r = t.taa_roll_right_del(taa_beg, taa_end)
     r.taa_range = taa_del_id(t, i1r, i2r, args)
     i1l, i2l = t.taa_roll_left_del(taa_beg, taa_end)
     r.append_info('left_align_protein=p.%s' %
                   taa_del_id(t, i1l, i2l, args))
-    r.append_info('unalign_protein=p.%s' % taa_del_id(
-        t, taa_beg, taa_end, args))
-    variant_protein_sequence_deletion(r, t, args, i1r, i2r)
+    r.append_info('unalign_protein=p.%s' %
+                  taa_del_id(t, taa_beg, taa_end, args))
+    variant_protein_seq_deletion(r, t, args, i1r, i2r)
 
 def del_coding_inframe(args, c1, c2, p1, p2, t, r):
 
@@ -399,11 +387,11 @@ def del_coding_frameshift(args, cbeg, cend, pbeg, pend, t, r):
     if not old_seq:
         raise IncompatibleTranscriptError("invalid_cDNA_position_%d;expect_[0_%d]" % cbeg_beg, len(t.seq))
 
-    ret = t.extend_taa_seq(cbeg.index, old_seq, new_seq)
-    if ret:
-        taa_pos, taa_ref, taa_alt, termlen = ret
-        r.taa_range = '%s%d%sfs*%d' % (aaf(taa_ref, args), taa_pos, aaf(taa_alt, args), termlen)
+    aae = t.extend_taa_seq(cbeg.index, old_seq, new_seq)
+    if aae:
+        r.taa_range = aae.format(args)
         r.csqn.append("Frameshift")
+        variant_protein_seq_fs(r, t, aae, args)
     else: # rare chance when stop codon seen before difference
         r.taa_range = '(=)'
         r.csqn.append("Synonymous")

transvar/frameshift.py

@@ -46,13 +46,10 @@ def fuzzy_match_deletion(t, codon, q, args):
             old_seq = t.seq[jb:]
             new_seq = t.seq[jb:j]+t.seq[j+ds:]
             tnuc_delseq = t.seq[j:j+ds]
-            ret = t.extend_taa_seq(j/3+1, old_seq, new_seq)
-            if ret:
-                _taa_pos, _taa_ref, _taa_alt, _termlen = ret
-                # print q.pos, q.ref, q.alt, q.stop_index, j, _taa_pos, _taa_ref, _taa_alt, _termlen
-                # print q.pos, q.ref, q.alt, type(q.stop_index), j, type(_taa_pos), type(_taa_ref), type(_taa_alt), type(_termlen)
-                if (q.ref == _taa_ref and ((not q.alt) or q.alt == _taa_alt)
-                    and q.stop_index == _termlen and q.pos == _taa_pos):
+            aae = t.extend_taa_seq(j/3+1, old_seq, new_seq)
+            if aae:
+                if (q.ref == aae.taa_ref and ((not q.alt) or q.alt == aae.taa_alt)
+                    and q.stop_index == aae.termlen and q.pos == aae.taa_pos):
                     t.ensure_position_array()
                     if t.strand == '+':
                         gnuc_beg, gnuc_end = t.np[j], t.np[j+ds-1]
@@ -117,17 +114,16 @@ def fuzzy_match_insertion_aa_change(t, j, ins_len, q):
     for _insseq in itertools.product(alphabets, repeat=ins_len):
         insseq = ''.join(_insseq)
         new_seq = t.seq[jb:j]+insseq+t.seq[j:]
-        ret = t.extend_taa_seq(j/3+1, old_seq, new_seq)
-        if ret:
-            _taa_pos, _taa_ref, _taa_alt, _termlen = ret
-            if (((not q.alt) or _taa_alt == q.alt) and q.ref == _taa_ref
-                and q.pos == _taa_pos and _termlen <= q.stop_index):
-                m = FuzzyInsMatch()
-                m.insseq = insseq
-                m.termlen = _termlen
-                match_seq.append(m)
-                if _termlen == q.stop_index:
-                    termlen_match = True
+        aae = t.extend_taa_seq(j/3+1, old_seq, new_seq)
+        if (aae and 
+            (((not q.alt) or aae.taa_alt == q.alt) and q.ref == aae.taa_ref
+             and q.pos == aae.taa_pos and aae.termlen <= q.stop_index)):
+            m = FuzzyInsMatch()
+            m.insseq = insseq
+            m.termlen = aae.termlen
+            match_seq.append(m)
+            if m.termlen == q.stop_index:
+                termlen_match = True
 
     # early stop when termlen also matches
     if termlen_match: