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# 8  
Old 10-10-2015
I have added other missing bases and AAcids to your awk code. Here is what I have now:
Code:
awk  '
BEGIN           {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 (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) {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) ACNT[a] += gsub (BASES[a], a)
                 print > "AminoAcids"
                }

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

Please pardon my question, but how do I run this from the command line? My input file that has the DNA sequences is called "input.txt"

This is how I tried to run it:
Code:
faizlo@faizlo $ awk -f rudic.awk input.txt 
awk: rudic.awk:1: awk  '
awk: rudic.awk:1:      ^ invalid char ''' in expression
awk: rudic.awk:1: awk  '
awk: rudic.awk:1:      ^ syntax error

I also tried to add:
Code:
#!/usr/bin/awk -f

at the beginning of the code but got the smae error(s.)

** rudic.awk is the script that has your awk script.
# 9  
Old 10-10-2015
Change the last line of rudic.awk from:
Code:
' file

to:
Code:
' input.txt

Then execute the script with:
Code:
sh rudic.awk

or make
Code:
rudic.awk

executable and execute it directly:
Code:
chmod +x rudic.awk
./rudic.awk

This User Gave Thanks to Don Cragun For This Post:
faizlo
# 10  
Old 10-11-2015
Interesting. I have done the executable step before but did not work!
It does now.
Thank you both for your help. I appreciate it.

---------- Post updated at 10:09 PM ---------- Previous update was at 10:03 PM ----------

I have one more question!

What should I do if I want the frequency from each line (sequence,) and not the total frequency of all sequences in the input file?
# 11  
Old 10-11-2015
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..
This User Gave Thanks to RudiC For This Post:
faizlo
# 12  
Old 10-11-2015
@RudiC:
Thank you so much for your help. I can't appreciate it more.
It will take me some time to understand the script as awk seems to be huge indeed.
Thank you so much again.
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