Fixing a shell script Post: 302957439

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Top Forums Shell Programming and Scripting Fixing a shell script Post 302957439 by RudiC on Sunday 11th of October 2015 04:44:24 AM

10-11-2015

Registered User

Would this do:

Code:

awk  -vDEBUG=1 '
BEGIN           {C1 = split ("UU[CU] UA[UC] GC[ACGU] GG[ACGU] CC[ACGU] AC[ACGU] GU[ACGU] CG[ACGU]|AG[AG] CU[ACGU]|UU[AG] "\
                                "UC[ACGU]|AG[CU] AU[ACU] AUG UA[AG]|UAG CA[AU] CA[AG] AA[UC] AA[AG] GA[CU] GA[AG] UG[CU] UGG", TMP1)
                 for (C2=i=split ("Phe Tyr Ala Gly Pro Thr Val Arg Leu Ser Ile Met STOP His Gln Asn Lys Asp Glu Cys Trp", TMP2); i > 0; i--)    {AACID[TMP2[i]]
                                                                                                                                                 BASES[TMP2[i]]=TMP1[i]
                                                                                                                                                }
                 if (DEBUG) {print C1, C2; for (t in TMP1) print TMP2[t], TMP1[t]}
                }


/^[     ]*$/    {EMP++
                 next
                }
/^>/            {$0=""
                }

                {print > "DNA.OUT"
                 gsub (/A/, "U")
                 gsub (/C/, "c")
                 gsub (/G/, "C")
                 gsub (/T/, "A")
                 gsub (/c/, "G")
                 print > "RNA.OUT"
                 gsub (/.../, "& ")
                 for (a in AACID)       {TMP = gsub (BASES[a], a)
                                         print NR, a, TMP                
                                         ACNT[a] += TMP
                                        }
                 print > "AminoAcids"
                }

END             {print "lines: ", NR-EMP
                 print "empty: ", EMP
                 for (a in ACNT) print a, ACNT[a]
                }
' file

?

---------- Post updated at 10:44 ---------- Previous update was at 10:25 ----------

A bit more structured approach:

Code:

awk  -vDEBUG=1 '
BEGIN           {Str1 = "UU[CU] UA[UC] GC[ACGU] GG[ACGU] CC[ACGU] AC[ACGU] GU[ACGU] CG[ACGU]|AG[AG] CU[ACGU]|UU[AG] "\
                        "UC[ACGU]|AG[CU] AU[ACU] AUG UA[AG]|UAG CA[AU] CA[AG] AA[UC] AA[AG] GA[CU] GA[AG] UG[CU] UGG" 
                 Str2 = "Phe Tyr Ala Gly Pro Thr Val Arg Leu Ser Ile Met STOP His Gln Asn Lys Asp Glu Cys Trp"
                 C1 = split (Str1, TMP1)
                 for (C2=i=split (Str2, TMP2); i > 0; i--)      {AACID[TMP2[i]]
                                                                 BASES[TMP2[i]]=TMP1[i]
                                                                }
                 if (DEBUG) {print C1, C2; for (t in TMP1) print TMP2[t], TMP1[t]}

                 C1 = split ("ACGTc", PAT, "")
                 C2 = split ("UcCAG", REP, "")
                 if (DEBUG) {print C1, C2; for (p in PAT) print PAT[p], REP[p]}
                }


/^[     ]*$/    {EMP++
                 next 
                }
/^>/            {$0=""
                }

                {print > "DNA.OUT" 
                 for (i=1; i<=C1; i++)  gsub (PAT[i], REP[i])
                 print > "RNA.OUT" 
                 gsub (/.../, "& ")
                 for (a in AACID)       {TMP = gsub (BASES[a], a)
                                         print NR, a, TMP
                                         ACNT[a] += TMP  
                                        }
                 print > "AminoAcids"
                }

END             {print "lines: ", NR-EMP
                 print "empty: ", EMP   
                 for (a in ACNT) print a, ACNT[a]
                }
' file

(The parentheses in Str1 were a heritage from a former version - not needed anymore)

Last edited by RudiC; 10-11-2015 at 06:18 AM..

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