insertion length limit for alignment

learnMSA/msa_hmm/AlignInsertions.py

@@ -6,7 +6,7 @@
 import sys
 
 
-def find_long_insertions_and_write_slice(fasta_file, lens, starts, name, directory, t = 20, k=2, verbose=True):
+def find_long_insertions_and_write_slice(fasta_file, lens, starts, name, directory, t = 20, k=2, max_insertions_len=500, verbose=True):
         """
         Finds insertions that have at least length t. If there are at least k of these sequences, writes them to file.
         Args: 
@@ -32,7 +32,7 @@ def find_long_insertions_and_write_slice(fasta_file, lens, starts, name, directo
                         if aa in segment:
                             only_non_standard_aa = False
                             break
-                    if only_non_standard_aa:
+                    if only_non_standard_aa or lengths[j] > max_insertions_len:
                         to_delete.append(j)
                     else:
                         slice_file.write(">"+fasta_file.seq_ids[which[j]]+"\n")

test/data/egf.out.fasta

@@ -1,24 +1,24 @@
 >1ixa
-..vdgdqCESN...PCLNGGSCK..-DD-IN..S..YECWCPFGFEGKNcel....................
+..vdgdqCESN...PCLNGGSCK..-DD...-IN..S.YECWCPFGFEGKNcel....................
 >1apo
-..kdgdqCEGH...PCLNQGHCK..-DG-IG..D..YTCTCAEGFEGKNcefstr.................
+..kdgdqCEGH...PCLNQGHCK..-DG...-IG..D.YTCTCAEGFEGKNcefstr.................
 >1urk
-.......QVPSnc.DCLNGGTCV..SNK-YF..SniHWCNCPKKFGGQHceidk..................
+......qVPSNc..DCLNGGTCV..-SNkyfS-N..I.HWCNCPKKFGGQHceidk..................
 >1fsb
-....tasCQDM...SCSKQGECL..-ET-IG..N..YTCSCYPGFYGPEceyvre.................
+....tasCQDM...SCSKQGECL..-ET...-IG..N.YTCSCYPGFYGPEceyvre.................
 >1esl
-......aCTNT...SCSGHGECV..-ET-IN..N..YTCKCDPGFSGLKceqiv..................
+......aCTNT...SCSGHGECV..-ET...-IN..N.YTCKCDPGFSGLKceqiv..................
 >1hre
-gtshlvkCAEKektFCVNGGECFmvKDL-SNpsR..YLCKCQPGFTGARctenvpmkvqnqekaeelyqk..
+gtshlvkCAEKektFCVNGGECFmvKDL...-SNpsR.YLCKCQPGFTGARctenvpmkvqnqekaeelyqk..
 >1epi
-..nsypgCPSSydgYCLNGGVCMh.IES-LD..S..YTCNCVIGYSGDRcqtrdlrwwelr...........
+..nsypgCPSSydgYCLNGGVCMh.IES...-LD..S.YTCNCVIGYSGDRcqtrdlrwwelr...........
 >4tgf
-vvshfndCPDShtqFCFH-GTCRf.LVQ-ED..K..PACVCHSGYVGARcehadlla...............
+vvshfndCPDShtqFCFH-GTCRf.LVQ...-ED..K.PACVCHSGYVGARcehadlla...............
 >1hcgb
-.......CSLD...NGDCDQFCH..-EE-QN..S..VVCSCARGYTLADngkaciptgpypcgkqtler...
+.......CSLD...NGDCDQFCH..-EE...-QN..S.VVCSCARGYTLADngkaciptgpypcgkqtler...
 >1dan1
-....gdqCASS...PCQNGGSCK..-DQ-LQ..S..YICFCLPAFEGRNcethkd.................
+....gdqCASS...PCQNGGSCK..-DQ...-LQ..S.YICFCLPAFEGRNcethkd.................
 >1dan2
-...dqliCVNE...NGGCEQYCS..-DH-TG..Tk.RSCRCHEGYSLLAdgvsctptveypcgkipile...
+...dqliCVNE...NGGCEQYCS..-DH...-TG..TkRSCRCHEGYSLLAdgvsctptveypcgkipile...
 >1rfnb
-.....mtCNIK...NGRCEQFCK..-NSADN..K..VVCSCTEGYRLAEnqkscepavpfpcgrvsvsqtsk
+.....mtCNIK...NGRCEQFCK..-NS...ADN..K.VVCSCTEGYRLAEnqkscepavpfpcgrvsvsqtsk